Hi, could anyone help me to sovle the following problem? I only want to do gene enrichment analysis for a non-model organism and ppy_GOannot.txt acquired from http://www.ebi.ac.uk/QuickGO/GAnnotation. library("GOstats") library("GSEABase") library("AnnotationDbi") ppyGO<-read.table("ppy_GOannot.txt",header=F) head(ppyGO) V1 V2 V3 1 GO:0001933 IEA A2BDH2 2 GO:0005507 IEA A2BDH2 3 GO:0005634 IEA A2BDH2 4 GO:0005730 IEA A2BDH2 5 GO:0005783 IEA A2BDH2 6 GO:0005794 IEA A2BDH2 goFrome <- GOFrame(ppyGO,organism = "Pongo abelii") Error in .testGOFrame(x, organism) : invalid GO Evidence codes: 'InterPro:IPR009003' 'InterPro:IPR001254|InterPro:IPR001314|InterPro:IPR018114' 'UniProtKB- KW:KW-0645' 'UniProtKB-KW:KW-0720' 'UniProtKB-KW:KW-0378' 'InterPro:IPR024886' 'UniProtKB-KW:KW-0807' 'InterPro:IPR000276' 'UniProtKB-KW:KW-0297' 'InterPro:IPR000725' 'UniProtKB-KW:KW-1003' 'UniProtKB-SubCell:SL-0039' 'InterPro:IPR000276|InterPro:IPR000725' 'UniProtKB-KW:KW-0552' 'UniProtKB-KW:KW-0472' 'InterPro:IPR000276|InterPro:IPR000725|InterPro:IPR017452' 'UniProtKB- KW:KW-0812' 'UniProtKB-KW:KW-0716' 'InterPro:IPR004072' 'InterPro:IPR004072|InterPro:IPR017452' 'InterPro:IPR015785' 'InterPro:IPR000719|InterPro:IPR001245' 'InterPro:IPR000719' 'InterPro:IPR011009' 'UniProtKB-KW:KW-0547' 'InterPro:IPR008280|InterPro:IPR018316' 'InterPro:IPR002453' 'InterPro :IPR002453|InterPro:IPR008280|InterPro:IPR017975|InterPro:IPR018316' 'UniProtKB-KW:KW-0342' 'UniProtKB-KW:KW-0963' 'UniProtKB-KW:KW-0206' 'InterPro:IPR000217|InterPro:IPR002453|InterPro:IPR017975' 'UniProtK sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GO.db_2.9.0 GSEABase_1.22.0 annotate_1.38.0 [4] GOstats_2.26.0 RSQLite_0.11.4 DBI_0.2-7 [7] graph_1.38.3 Category_2.26.0 AnnotationDbi_1.22.6 [10] Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] AnnotationForge_1.2.2 genefilter_1.42.0 IRanges_1.18.2 [4] RBGL_1.36.2 splines_3.0.1 stats4_3.0.1 [7] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 [10] xtable_1.7-1 Thank you! Best wish, Zhidong Yuan [[alternative HTML version deleted]]

This error is complaining about a value for the middle column of the data.frame supplied to GOFrame. I can't verify this though since I don't know which file from http://www.ebi.ac.uk/QuickGO/GAnnotation is the one you labeled as ppy_GOannot.txt (presumably GO terms for Orangutan), and the 1st 6 lines of your object all look basically OK. Have you checked if any of the rows in your data.frame equal to the values that the error is complaining about? Or could you maybe give me more specific directions to the file you are using? Also, the third column of what you show could be a bit risky since those look like gene symbols. And gene symbols are not good gene IDs. Marc On 08/05/2013 03:08 AM, Zhidong Yuan wrote: > GOFrame(ppyGO,organism = "Pongo abelii")